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(-) Description

Title :  CRYSTAL STRUCTURE OF DICAMBA MONOOXYGENASE WITH NON-HEME IRON
 
Authors :  T. J. Rydel, E. J. Sturman, F. Moshiri, G. R. Brown, Y. Qi
Date :  27 Mar 09  (Deposition) - 28 Jul 09  (Release) - 06 Oct 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Rieske Non-Heme Iron Oxygenase, Electron Transport, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. L. D'Ordine, T. J. Rydel, M. J. Storek, E. J. Sturman, F. Moshiri, R. K. Bartlett, G. R. Brown, R. J. Eilers, C. Dart, Y. Qi, S. Flasinski, S. J. Franklin
Dicamba Monooxygenase: Structural Insights Into A Dynamic Rieske Oxygenase That Catalyzes An Exocyclic Monooxygenation.
J. Mol. Biol. V. 392 481 2009
PubMed-ID: 19616009  |  Reference-DOI: 10.1016/J.JMB.2009.07.022
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DDMC
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B(+)(KANAMYCIN RESISTANT)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DDMC
    Organism Common: PSEUDOMONAS MALTOPHILIA
    Organism Scientific: STENOTROPHOMONAS MALTOPHILIA
    Organism Taxid: 40324

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric/Biological Unit (3, 9)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
2FE2Ligand/IonFE (III) ION
3FES3Ligand/IonFE2/S2 (INORGANIC) CLUSTER

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:49 , HIS A:51 , ARG A:52 , CYS A:68 , TYR A:70 , HIS A:71 , LEU A:73BINDING SITE FOR RESIDUE FES A 501
2AC2SOFTWAREASN A:154 , HIS A:160 , HIS A:165 , ASP A:294 , ACT A:650BINDING SITE FOR RESIDUE FE A 502
3AC3SOFTWAREHIS A:160 , HIS A:165 , LEU A:290 , ASP A:294 , FE A:502 , ACT A:651BINDING SITE FOR RESIDUE ACT A 650
4AC4SOFTWAREASN A:230 , HIS A:251 , TRP A:285 , ACT A:650 , HOH A:977BINDING SITE FOR RESIDUE ACT A 651
5AC5SOFTWARECYS B:49 , HIS B:51 , ARG B:52 , CYS B:68 , TYR B:70 , HIS B:71 , LEU B:73BINDING SITE FOR RESIDUE FES B 501
6AC6SOFTWAREASN B:154 , HIS B:160 , HIS B:165 , ASP B:294 , ACT B:652BINDING SITE FOR RESIDUE FE B 502
7AC7SOFTWAREHIS B:165 , LEU B:290 , ASP B:294 , FE B:502BINDING SITE FOR RESIDUE ACT B 652
8AC8SOFTWAREASN B:230 , HIS B:251 , TRP B:285 , HOH B:787 , HOH B:870BINDING SITE FOR RESIDUE ACT B 653
9AC9SOFTWARECYS C:49 , HIS C:51 , ARG C:52 , CYS C:68 , HIS C:71 , LEU C:73BINDING SITE FOR RESIDUE FES C 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3GTE)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3GTE)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3GTE)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3GTE)

(-) Exons   (0, 0)

(no "Exon" information available for 3GTE)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:341
 aligned with Q5S3I3_STEMA | Q5S3I3 from UniProtKB/TrEMBL  Length:339

    Alignment length:341
                                                                                                                                                                                                                                                                                                                                                                            339  
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330        |- 
         Q5S3I3_STEMA     1 MTFVRNAWYVAALPEELSEKPLGRTILDTPLALYRQPDGVVAALLDICPHRFAPLSDGILVNGHLQCPYHGLEFDGGGQCVHNPHGNGARPASLNVRSFPVVERDALIWIWPGDPALADPGAIPDFGCRVDPAYRTVGGYGHVDCNYKLLVDNLMDLGHAQYVHRANAQTDAFDRLEREVIVGDGEIQALMKIPGGTPSVLMAKFLRGANTPVDAWNDIRWNKVSAMLNFIAVAPEGTPKEQSIHSRGTHILTPETEASCHYFFGSSRNFGIDDPEMDGVLRSWQAQALVKEDKVVVEAIERRRAYVEANGIRPAMLSCDEAAVRVSREIEKLEQLEAA--   -
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeehhhhh....eeeee..eeeeeee.....eeeee........hhhhheee..eee......ee.....eee........hhhhh.....eeee..eeee...hhhhhhhhhh..hhhhhh...eeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeeeeee..eeeeeeee.....hhhhhhhh......eeeeeeeeee...eeeeeeeeee........eeeeeeeeeeeee..eeeeeeeeee.....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gte A   2 ATFVRNAWYVAALPEELSEKPLGRTILDTPLALYRQPDGVVAALLDICPHRFAPLSDGILVNGHLQCPYHGLEFDGGGQCVHNPHGNGARPASLNVRSFPVVERDALIWIWPGDPALADPGAIPDFGCRVDPAYRTVGGYGHVDCNYKLLVDNLMDLGHAQYVHRANAQTDAFDRLEREVIVGDGEIQALMKIPGGTPSVLMAKFLRGANTPVDAWNDIRWNKVSAMLNFIAVAPEGTPKEQSIHSRGTHILTPETEASCHYFFGSSRNFGIDDPEMDGVLRSWQAQALVKEDKVVVEAIERRRAYVEANGIRPAMLSCDEAAVRVSREIEKLEQLEAARL 342
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341 


Chain B from PDB  Type:PROTEIN  Length:341
 aligned with Q5S3I3_STEMA | Q5S3I3 from UniProtKB/TrEMBL  Length:339

    Alignment length:341
                                                                                                                                                                                                                                                                                                                                                                            339  
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330        |- 
         Q5S3I3_STEMA     1 MTFVRNAWYVAALPEELSEKPLGRTILDTPLALYRQPDGVVAALLDICPHRFAPLSDGILVNGHLQCPYHGLEFDGGGQCVHNPHGNGARPASLNVRSFPVVERDALIWIWPGDPALADPGAIPDFGCRVDPAYRTVGGYGHVDCNYKLLVDNLMDLGHAQYVHRANAQTDAFDRLEREVIVGDGEIQALMKIPGGTPSVLMAKFLRGANTPVDAWNDIRWNKVSAMLNFIAVAPEGTPKEQSIHSRGTHILTPETEASCHYFFGSSRNFGIDDPEMDGVLRSWQAQALVKEDKVVVEAIERRRAYVEANGIRPAMLSCDEAAVRVSREIEKLEQLEAA--   -
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeehhhhh....eeeee..eeeeeee.....eeeee........hhhhheee..eee......ee.....eee........hhhhh.....eeee..eeee...hhhhhhhhhh..hhhhhh...eeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhh..hhhhheeeeee...eeeeeeeeeee..hhhhhhhh......eeeeeeeeee...eeeeeeeeee...hhhhheeeeeeeeeeeee..eeeeeeeeee.....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gte B   2 ATFVRNAWYVAALPEELSEKPLGRTILDTPLALYRQPDGVVAALLDICPHRFAPLSDGILVNGHLQCPYHGLEFDGGGQCVHNPHGNGARPASLNVRSFPVVERDALIWIWPGDPALADPGAIPDFGCRVDPAYRTVGGYGHVDCNYKLLVDNLMDLGHAQYVHRANAQTDAFDRLEREVIVGDGEIQALMKIPGGTPSVLMAKFLRGANTPVDAWNDIRWNKVSAMLNFIAVAPEGTPKEQSIHSRGTHILTPETEASCHYFFGSSRNFGIDDPEMDGVLRSWQAQALVKEDKVVVEAIERRRAYVEANGIRPAMLSCDEAAVRVSREIEKLEQLEAARL 342
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341 


Chain C from PDB  Type:PROTEIN  Length:332
 aligned with Q5S3I3_STEMA | Q5S3I3 from UniProtKB/TrEMBL  Length:339

    Alignment length:341
                                                                                                                                                                                                                                                                                                                                                                            339  
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330        |- 
         Q5S3I3_STEMA     1 MTFVRNAWYVAALPEELSEKPLGRTILDTPLALYRQPDGVVAALLDICPHRFAPLSDGILVNGHLQCPYHGLEFDGGGQCVHNPHGNGARPASLNVRSFPVVERDALIWIWPGDPALADPGAIPDFGCRVDPAYRTVGGYGHVDCNYKLLVDNLMDLGHAQYVHRANAQTDAFDRLEREVIVGDGEIQALMKIPGGTPSVLMAKFLRGANTPVDAWNDIRWNKVSAMLNFIAVAPEGTPKEQSIHSRGTHILTPETEASCHYFFGSSRNFGIDDPEMDGVLRSWQAQALVKEDKVVVEAIERRRAYVEANGIRPAMLSCDEAAVRVSREIEKLEQLEAA--   -
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeehhhhh....eeeee..eeeeeee.....eeeee........hhhhheee..eee......ee.....eee........hhhhh.....eeee..eeee...hhhhhhhhhh..hhhhhh...eeeeeeeee..hhhhhhhhhhh....hhhhh.---------..eeeee...eeeeeeeee.......hhhhhh.....eeeeeeeeee...eeeeeeeeee...hhhhheeeeeeeeeeeee..eeeeeeeeee.....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gte C   2 ATFVRNAWYVAALPEELSEKPLGRTILDTPLALYRQPDGVVAALLDICPHRFAPLSDGILVNGHLQCPYHGLEFDGGGQCVHNPHGNGARPASLNVRSFPVVERDALIWIWPGDPALADPGAIPDFGCRVDPAYRTVGGYGHVDCNYKLLVDNLMDLGHAQYVHRA---------LEREVIVGDGEIQALMKIPGGTPSVLMAKFLRGANTPVDAWNDIRWNKVSAMLNFIAVAPEGTPKEQSIHSRGTHILTPETEASCHYFFGSSRNFGIDDPEMDGVLRSWQAQALVKEDKVVVEAIERRRAYVEANGIRPAMLSCDEAAVRVSREIEKLEQLEAARL 342
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161     |   -     | 181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341 
                                                                                                                                                                                               167       177
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3GTE)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3GTE)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3GTE)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (Q5S3I3_STEMA | Q5S3I3)
molecular function
    GO:0051537    2 iron, 2 sulfur cluster binding    Interacting selectively and non-covalently with a 2 iron, 2 sulfur (2Fe-2S) cluster; this cluster consists of two iron atoms, with two inorganic sulfur atoms found between the irons and acting as bridging ligands.
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0051536    iron-sulfur cluster binding    Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0016708    oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of two atoms of oxygen into one donor    Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from NADH or NADPH and one other donor, and two atoms of oxygen are incorporated into one donor.
biological process
    GO:0019439    aromatic compound catabolic process    The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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        Q5S3I3_STEMA | Q5S3I3: 3gb4 3gke 3gl0 3gl2 3gob 3gts

(-) Related Entries Specified in the PDB File

3gb4 CRYSTAL STRUCTURE OF DICAMBA MONOOXYGENASE WITH NON-HEME COBALT AND DICAMBA
3gob CRYSTAL STRUCTURE OF DICAMBA MONOOXYGENASE WITH NON-HEME COBALT AND DCSA
3gts CRYSTAL STRUCTURE OF DICAMBA MONOOXYGENASE WITH NON-HEME IRON AND DICAMBA